<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I have installed Torque 2.5.10 on our systems and since then we have had problems with PBS variables like PBS_NODEFILE, PBS_JOBID, PBS_JOBNAME, PBS_O_WORKDIR, etc. Surprisingly, on the same node it works ok for one user and it doesn't work for another user. Right now to solve this I am sourcing another script into every pbs script through qsub wrapper. But this line comes only after pbs directives. So, if anyone mentions these variables in #PBS -e and #PBS -o directives, then jobs are failing.</div><div><br></div><div>Is there anyone facing the same problem? I am not sure whether this issue would be taken care of if I installed 2.5.11 as I didn't see anything regarding this in the changelogs.</div><div><br></div><div>Here is one example. This user is always having the problems with PBS_NODEFILE variable (user runs parallel jobs with scripts in tcsh). For now, it's ok as I asked her to mention the absolute path for #PBS -e and -o lines and PBS_NODEFILE is defined by the script added to pbs script by qsub wrapper ( the added script finds the PBS_NODEFILE in /opt/torque/aux/ and exports the variable PBS_NODEFILE with the filename)</div><div><br></div><div>Script emails me whenever it doesn't find this variable. This is an example:</div><div><br></div><div><br></div><div>on host compute-8-2.local for the parallel job.<br>
"env | grep PBS" output<br>
PBS_O_QUEUE=p12<br>
PBS_O_HOST=login-0-1.local<br>
PBS_O_HOME=/home/gs****<br>
PBS_O_LANG=en_US.iso885915<br>
PBS_O_LOGNAME=gs****<br>
PBS_O_PATH=/home/gs****/bin:/<wbr>bin:/share/apps/grace/5.1.22/<wbr>intel/grace/bin:/share/apps/<wbr>autodocksuite/4.2.1/intel/bin:<wbr>/share/apps/grace/5.1.22/<wbr>intel/grace/bin:/share/apps/<wbr>apbs/1.1.0/intel/bin:/share/<wbr>apps/gromacs/4.0.5/intel-<wbr>mvapich/bin:/share/apps/<wbr>amber11/intel-mvapich/amber11/<wbr>/bin:/share/apps/python/2.6.4/<wbr>gnu/bin:/share/apps/gromacs/4.<wbr>0.5/intel-mvapich/bin:/share/<wbr>apps/amber11/intel-mvapich/<wbr>amber11/exe:/usr/mpi/intel/<wbr>mvapich-1.1.0/bin:/share/apps/<wbr>matlab/R2009b/bin:/share/apps/<wbr>mathematica/7.0/Executables/:/<wbr>share/apps/vmd/1.8.7/:/share/<wbr>apps/molden/4.7/gnu:/share/<wbr>apps/mpiexec/0.84/gnu/bin:/<wbr>share/apps/gaussian/G03-E01/<wbr>intel/g03:/share/apps/intel/<wbr>Compiler/11.1/046/bin/intel64:<wbr>/usr/kerberos/bin:/usr/java/<wbr>latest/bin:/usr/local/bin:/<wbr>bin:/usr/bin:/opt/ganglia/bin:<wbr>/opt/ganglia/sbin:/opt/maui/<wbr>bin:/opt/torque/bin:/opt/<wbr>torque/sbin:/opt/rocks/bin:/<wbr>opt/rocks/sbin:/opt/dell/<wbr>srvadmin/bin:/opt/torque/bin:/<wbr>opt/torque/sbin:/home/gs****/<wbr>jobscript/gromacs/<wbr>Hpluplus2oplsaa/:/share/apps/<wbr>gromacs/4.0.5/i<br>
&nbsp;ntel-mvapich/bin:/home/gs****/<wbr>coarse-grain/ElNeDyn:/home/<wbr>gs****/coarse-grain:/home/<wbr>gs****/jobscript/:/home/<wbr>gs****/jobscript/gromacs/<wbr>coarse-grain/:/home/gs****/<wbr>jobscript/gromacs/:/home/<wbr>gs****/nedit/:/share/apps/<wbr>mmtsb_toolset/intel/bin:/<wbr>share/apps/mmtsb_toolset/<wbr>intel/perl:/share/apps/dssp/<wbr>intel/dsspcmbi:/share/apps/<wbr>python/2.6.4/gnu/bin:/share/<wbr>apps/time-scapes/1.2.2/intel/<wbr>test:/share/apps/time-scapes/<wbr>1.2.2/intel/bin:/share/apps/<wbr>pymol/1.2r3pre/gnu/bin:/home/<wbr>gs****/jobscript/gromacs/<wbr>Hpluplus2amber99sb/:/home/<wbr>gs****/jobscript/perl/:/share/<wbr>apps/dssp/intel/:/home/gs****/<wbr>jobscript/autodocktools/:/<wbr>share/apps/mmtsb_toolset/perl/<wbr>:/home/gs****/jobscript/<wbr>docking:/share/apps/tinker/4.<wbr>2/intel/bin/:/home/gs****/bin<br>
PBS_O_MAIL=/var/spool/mail/<wbr>gs****<br>
PBS_O_SHELL=/bin/bash<br>
PBS_SERVER=*****<a href="http://crunch.its.nyu.edu" target="_blank">.its.nyu.edu</a><br>
PBS_O_WORKDIR=/scratch/gs****/<wbr>amber/ache.somSER/mdrunE199H/<wbr>qm-mm-large3WAT/methylMIG-<wbr>singleRC/qmmmMD/MD.0.24.80<br>
PBS_JOBNAME=MD.0.24.80<br>
PBS_JOBID=219825.crunch.local<br>
PBS_QUEUE=p12<br>
PBS_JOBCOOKIE=<wbr>C4EA940FBC845949E6DB4D1BD7855E<wbr>A0<br>
PBS_NODENUM=0</div><div><br></div><div><br></div><div>I configured torque like this:</div><div><br></div><div><div>./configure --prefix=/opt/torque --libdir=/opt/torque/lib64 --with-default-server=crunch.its.nyu.edu --with-server-home=/opt/torque --enable-docs --enable-syslog --disable-gui --enable-blcr --disable-spool --enable-cpuset --enable-geometry-requests --enable-server-xml --with-pam=/lib64/security</div></div><div><br></div><div>If it's happening to anyone else, please respond to this email.</div><div><br></div><div>Thanks,</div><div>Sreedhar.</div><div><br></div></body></html>